PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID KN540218.1_FGP001
Organism
Oryza longistaminata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
Family C3H
Protein Properties Length: 207aa    MW: 23773.6 Da    PI: 5.3153
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KN540218.1_FGP001genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH30.46.5e-101438226
                       -S---SGGGGTS--TTTTT-SS-SS CS
            zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                       ++++C+f+++ G C++GdrC++ H 
  KN540218.1_FGP001 14 DRVNCPFYFKIGACRHGDRCSRLHN 38
                       6899********************7 PP
2zf-CCCH21.44.4e-07150173226
                        -S---SGGGGTS--TTTTT-SS-SS CS
            zf-CCCH   2 ktelCrffartGtCkyGdrCkFaHg 26 
                        +++ Cr + +   C++G+ C+F+H+
  KN540218.1_FGP001 150 REATCRQYEE-NSCNRGGYCNFMHV 173
                        6789**9999.*************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.0651240IPR000571Zinc finger, CCCH-type
SMARTSM003560.00681339IPR000571Zinc finger, CCCH-type
PfamPF006421.7E-71438IPR000571Zinc finger, CCCH-type
PRINTSPR018489.3E-641837IPR009145U2 auxiliary factor small subunit
PRINTSPR018489.3E-643757IPR009145U2 auxiliary factor small subunit
CDDcd125391.96E-6544145No hitNo description
PROSITE profilePS501029.74644146IPR000504RNA recognition motif domain
Gene3DG3DSA:3.30.70.3307.8E-2544145IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018489.3E-647590IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549283.39E-1677149IPR012677Nucleotide-binding alpha-beta plait domain
PfamPF000762.2E-483139IPR000504RNA recognition motif domain
PRINTSPR018489.3E-64103125IPR009145U2 auxiliary factor small subunit
PRINTSPR018489.3E-64130154IPR009145U2 auxiliary factor small subunit
SMARTSM003560.021148174IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.798148175IPR000571Zinc finger, CCCH-type
PfamPF006425.3E-5150174IPR000571Zinc finger, CCCH-type
PRINTSPR018489.3E-64165177IPR009145U2 auxiliary factor small subunit
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000398Biological ProcessmRNA splicing, via spliceosome
GO:0089701Cellular ComponentU2AF
GO:0000166Molecular Functionnucleotide binding
GO:0003723Molecular FunctionRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 207 aa     Download sequence    Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNRP TISPTLVFAN MYQHPDMITP  60
GVDAQGQPID PRQMQEHFED FYEDIFEELS KFGEIENLNV CDNLADHMIG NVYVQLREED  120
QAAAAHTALQ GRFYSGRPII VDFSPVTDFR EATCRQYEEN SCNRGGYCNF MHVKQIGTWE  180
GSEEKTLWPL QKATTRQEPQ PKPKPTP
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A5e-6811751170Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtNecessary for the splicing of pre-mRNA. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapKN540218.1_FGP001
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCP0126090.0CP012609.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025816779.11e-128splicing factor U2af small subunit B-like
RefseqXP_025816780.11e-128splicing factor U2af small subunit B-like
RefseqXP_025816781.11e-128splicing factor U2af small subunit B-like
RefseqXP_025816782.11e-128splicing factor U2af small subunit B-like
SwissprotQ6AUG01e-123U2AFB_ORYSJ; Splicing factor U2af small subunit B
TrEMBLI1NQH71e-154I1NQH7_ORYGL; Uncharacterized protein
STRINGORGLA01G0211700.11e-155(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP126133
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.12e-37C3H family protein
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]
  3. Domon C,Lorković ZJ,Valcárcel J,Filipowicz W
    Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants.
    J. Biol. Chem., 1998. 273(51): p. 34603-10
    [PMID:9852132]